Merge pull request #685 from henrypinkard/acqengpy

Python backend + new APIs

docs/source/application_notebooks/PSF_viewer.py

@@ -44,7 +44,7 @@
 import napari
 from napari.qt import thread_worker
 from magicgui import magicgui
-from pycromanager import Acquisition, multi_d_acquisition_events
+from pycromanager import JavaBackendAcquisition, multi_d_acquisition_events
 # open napari in an extra window, only needed for jupyter notebooks
 #%gui qt
 
@@ -166,9 +166,9 @@ def acquire_data(z_range):
     """ micro-manager data acquisition. Creates acquisition events for z-stack.
         This example: use custom events, not multi_d_acquisition because the 
         z-stage is not run from micro-manager but controlled via external DAQ."""
-    with Acquisition(directory=None, name=None, 
-                     show_display=True, 
-                     image_process_fn = grab_image) as acq:
+    with JavaBackendAcquisition(directory=None, name=None,
+                                show_display=True,
+                                image_process_fn = grab_image) as acq:
         events = []
         for index, z_um in enumerate(np.linspace(z_range[0], z_range[1], z_range[2])):
             evt = {"axes": {"z_ext": index}, "z_ext": z_um}
@@ -182,9 +182,9 @@ def acquire_multid(z_range):
         from micro-manager.
         Unless hardware triggering is set up in micro-manager, this will be fairly slow:
         micro-manager does not sweep the z-stage, but acquires plane by plane. """
-    with Acquisition(directory=None, name=None, 
-                     show_display=False, 
-                     image_process_fn = grab_image) as acq:
+    with JavaBackendAcquisition(directory=None, name=None,
+                                show_display=False,
+                                image_process_fn = grab_image) as acq:
         events = multi_d_acquisition_events(z_start=z_range[0], z_end=z_range[1], 
                                             z_step=(z_range[1]-z_range[0])/(z_range[2]-1))
         acq.acquire(events)

java/pom.xml

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.pycro-manager</groupId>
     <artifactId>PycroManagerJava</artifactId>
-     <version>0.43.1</version>
+     <version>0.44.0</version>
     <packaging>jar</packaging>
     <name>Pycro-Manager Java</name>
     <description>The Java components of Pycro-Manager</description>
@@ -54,7 +54,7 @@
       <dependency>
          <groupId>org.micro-manager.acqengj</groupId>
          <artifactId>AcqEngJ</artifactId>
-     <version>0.32.2</version>
+     <version>0.33.0</version>
       </dependency>
       <dependency>
          <groupId>org.micro-manager.ndviewer</groupId>
@@ -64,7 +64,7 @@
       <dependency>
          <groupId>org.micro-manager.ndtiffstorage</groupId>
          <artifactId>NDTiffStorage</artifactId>
-     <version>2.14.0</version>
+     <version>2.15.1</version>
       </dependency>
   </dependencies>
 

java/src/main/java/org/micromanager/explore/ExploreAcqUIAndStorage.java

@@ -358,7 +358,7 @@ protected ExploreMouseListener createMouseListener() {
       return new ExploreMouseListener(acq_, display_, logger_);
    }
 
-   public void putImage(final TaggedImage taggedImg) {
+   public Object putImage(final TaggedImage taggedImg) {
 
       String channelName = (String) AcqEngMetadata.getAxes(taggedImg.tags).get("channel");
       boolean newChannel = !channelNames_.contains(channelName);
@@ -399,6 +399,7 @@ public void run() {
             }
          });
       }
+      return null;
    }
 
 

java/src/main/java/org/micromanager/internal/zmq/ZMQServer.java

@@ -42,7 +42,7 @@ public class ZMQServer extends ZMQSocketWrapper {
    private static Function<Class, Object> classMapper_;
    private static ZMQServer mainServer_;
    static boolean debug_ = false;
-   private Consumer<String> debugLogger_;
+   private static Consumer<String> debugLogger_;
 
    //for testing
 //   public static void main(String[] args) {
@@ -76,6 +76,9 @@ public ZMQServer(Collection<ClassLoader> cls, Function<Class, Object> classMappe
    public ZMQServer(Collection<ClassLoader> cls, Function<Class, Object> classMapper,
                     String[] excludePaths, Consumer<String> debugLogger, int port) throws URISyntaxException, UnsupportedEncodingException {
       super(SocketType.REP, port);
+      mainServer_ = this;
+      debugLogger_ = debugLogger;
+
       classMapper_ = classMapper;
       util_ = new ZMQUtil(cls, excludePaths);
 
@@ -89,7 +92,6 @@ public ZMQServer(Collection<ClassLoader> cls, Function<Class, Object> classMappe
             packages_.addAll(Stream.of(Package.getPackages()).map(p -> p.getName()).collect(Collectors.toList()));
          }
       }
-      debugLogger_ = debugLogger;
    }
 
    public static ZMQServer getMasterServer() {
@@ -440,8 +442,8 @@ private JSONObject runMethod(Object obj, JSONObject message, boolean staticMetho
    protected JSONObject parseAndExecuteCommand(JSONObject request) throws Exception {
       JSONObject reply;
       switch (request.getString("command")) {
-         case "connect": {//Connect to master server
-            mainServer_ = this;
+         case "connect": {
+            // Connect to the server
             debug_ = request.getBoolean("debug");
             //Called by master process
             reply = new JSONObject();

java/src/main/java/org/micromanager/lightsheet/StackResamplersImageProcessor.java

@@ -1,5 +1,6 @@
 package org.micromanager.lightsheet;
 
+import java.util.concurrent.BlockingQueue;
 import mmcorej.TaggedImage;
 import mmcorej.org.json.JSONException;
 import mmcorej.org.json.JSONObject;
@@ -73,7 +74,7 @@ public StackResamplersImageProcessor(int mode, double theta, double cameraPixelS
    /**
     * For testing purposes only
     */
-   LinkedBlockingDeque<TaggedImage> getOutputQueue() {
+   BlockingQueue<TaggedImage> getOutputQueue() {
       return sink_;
    }
 

java/src/main/java/org/micromanager/remote/RemoteAcquisitionFactory.java

@@ -44,12 +44,10 @@ public RemoteAcquisition createAcquisition(String dir, String name, boolean show
                                               int savingQueueSize, boolean debug) {
       RemoteEventSource eventSource = new RemoteEventSource();
       RemoteViewerStorageAdapter adapter = null;
-      if (name != null && dir != null) {
-         // Saving to disk
-         adapter = new RemoteViewerStorageAdapter(showViewer, dir, name, false, 0,0,
-                 null, savingQueueSize);
 
-      }
+      adapter = new RemoteViewerStorageAdapter(showViewer, dir, name, false, 0,0,
+              null, savingQueueSize);
+
       return new RemoteAcquisition(eventSource, adapter, debug);
    }
 

java/src/main/java/org/micromanager/remote/RemoteImageProcessor.java

@@ -5,6 +5,7 @@
  */
 package org.micromanager.remote;
 
+import java.util.concurrent.BlockingQueue;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.LinkedBlockingDeque;
@@ -30,7 +31,7 @@ public class RemoteImageProcessor implements TaggedImageProcessor {
 
    private ExecutorService pushExecutor_, pullExecutor_;
 
-   volatile LinkedBlockingDeque<TaggedImage> source_, sink_;
+   volatile BlockingQueue<TaggedImage> source_, sink_;
 
    ZMQPushSocket<TaggedImage> pushSocket_;
    ZMQPullSocket<TaggedImage> pullSocket_;
@@ -97,7 +98,7 @@ public void startPush() {
          while (true) {
             if (source_ != null) {
                try {
-                  TaggedImage img = source_.takeFirst();
+                  TaggedImage img = source_.take();
                   pushSocket_.push(img);
                   if (img.tags == null && img.pix == null) {
                      // all images have been pushed
@@ -124,7 +125,7 @@ public void startPull() {
             if (sink_ != null) {
                try {
                   TaggedImage ti = pullSocket_.next();
-                  sink_.putLast(ti);
+                  sink_.put(ti);
                   if (ti.pix == null && ti.tags == null) {
                      pullExecutor_.shutdown();
                      break;
@@ -146,6 +147,12 @@ public void startPull() {
    @Override
    public void setAcqAndDequeues(AcquisitionAPI acq,
                            LinkedBlockingDeque<TaggedImage> source, LinkedBlockingDeque<TaggedImage> sink) {
+      // This is deprecated, remove in a future version once its taken out of API
+   }
+
+   @Override
+   public void setAcqAndQueues(AcquisitionAPI acq, BlockingQueue<TaggedImage> source,
+                               BlockingQueue<TaggedImage> sink) {
       source_ = source;
       sink_ = sink;
    }

java/src/main/java/org/micromanager/remote/RemoteNotificationHandler.java

@@ -9,9 +9,7 @@
 import org.micromanager.acqj.api.AcqNotificationListener;
 import org.micromanager.acqj.api.AcquisitionAPI;
 import org.micromanager.acqj.main.AcqNotification;
-import org.micromanager.acqj.main.Acquisition;
 import org.micromanager.internal.zmq.ZMQPushSocket;
-import org.micromanager.ndtiffstorage.IndexEntryData;
 
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -55,6 +53,8 @@ public void run() {
    public void start() {
       //constantly poll the socket for more event sequences to submit
       executor_.submit(() -> {
+         boolean eventsFinished = false;
+         boolean dataSinkFinished = false;
          while (true) {
             AcqNotification e = null;
             try {
@@ -66,8 +66,14 @@ public void start() {
             }
 
             pushSocket_.push(e);
-            if (e.isAcquisitionFinishedNotification()) {
-               return;
+            if (e.isAcquisitionEventsFinishedNotification()) {
+               eventsFinished = true;
+            }
+            if (e.isDataSinkFinishedNotification()) {
+               dataSinkFinished = true;
+            }
+            if (eventsFinished && dataSinkFinished) {
+               break;
             }
          }
       });
@@ -80,7 +86,8 @@ public void postNotification(AcqNotification n) {
 
    /**
     * Called by the python side to signal that the final shutdown signal has been received
-    * and that the push socket can be closed
+    * and that the push socket can be closed. Because otherwise it wouldn't be possible
+    * to know when the ZMQ push socket has finished doing its thing
     */
    public void notificationHandlingComplete() {
       executor_.submit(() -> {

java/src/main/java/org/micromanager/remote/RemoteStorageMonitor.java

@@ -19,6 +19,7 @@
  * A class that broadcasts information about images that have finsihed saving to disk
  * @author henrypinkard
  */
+@Deprecated
 public class RemoteStorageMonitor implements ImageWrittenListener {
 
    private ZMQPushSocket<IndexEntryData> pushSocket_;

java/src/main/java/org/micromanager/remote/RemoteViewerStorageAdapter.java

@@ -11,6 +11,8 @@
 import org.micromanager.acqj.api.AcqEngJDataSink;
 import org.micromanager.acqj.main.Acquisition;
 import org.micromanager.acqj.internal.Engine;
+import org.micromanager.ndtiffstorage.IndexEntryData;
+import org.micromanager.ndtiffstorage.NDRAMStorage;
 import org.micromanager.ndtiffstorage.NDTiffStorage;
 import org.micromanager.ndtiffstorage.MultiresNDTiffAPI;
 import org.micromanager.ndtiffstorage.NDTiffAPI;
@@ -34,8 +36,8 @@ class RemoteViewerStorageAdapter implements NDViewerDataSource, AcqEngJDataSink,
 
    private volatile NDViewerAPI viewer_;
    private volatile Acquisition acq_;
-   private volatile MultiresNDTiffAPI storage_;
-   private final boolean showViewer_, storeData_, xyTiled_;
+   private volatile NDTiffAPI storage_;
+   private final boolean showViewer_, xyTiled_;
    private final int tileOverlapX_, tileOverlapY_;
    private String dir_;
    private String name_;
@@ -58,7 +60,6 @@ public RemoteViewerStorageAdapter(boolean showViewer, String dataStorageLocation
                                      int tileOverlapY,
                                      Integer maxResLevel, int savingQueueSize) {
       showViewer_ = showViewer;
-      storeData_ = dataStorageLocation != null;
       xyTiled_ = xyTiled;
       dir_ = dataStorageLocation;
       name_ = name;
@@ -71,13 +72,19 @@ public RemoteViewerStorageAdapter(boolean showViewer, String dataStorageLocation
    public void initialize(Acquisition acq, JSONObject summaryMetadata) {
       acq_ = acq;
 
-      if (storeData_) {
-         if (xyTiled_) {
-            //tiled datasets have a fixed, acquisition-wide image size
-            AcqEngMetadata.setWidth(summaryMetadata, (int) Engine.getCore().getImageWidth());
-            AcqEngMetadata.setHeight(summaryMetadata, (int) Engine.getCore().getImageHeight());
-         }
 
+      if (xyTiled_) {
+         //tiled datasets have a fixed, acquisition-wide image size
+         AcqEngMetadata.setWidth(summaryMetadata, (int) Engine.getCore().getImageWidth());
+         AcqEngMetadata.setHeight(summaryMetadata, (int) Engine.getCore().getImageHeight());
+      }
+
+      if (dir_ == null) {
+         storage_ = new NDRAMStorage(summaryMetadata);
+         if (name_ == null) {
+            name_ = "In RAM acquisition";
+         }
+      } else {
          storage_ = new NDTiffStorage(dir_, name_,
                summaryMetadata, tileOverlapX_, tileOverlapY_,
                xyTiled_, maxResLevel_, savingQueueSize_,
@@ -87,7 +94,6 @@ public void initialize(Acquisition acq, JSONObject summaryMetadata) {
                }) : null, true
          );
          name_ = storage_.getUniqueAcqName();
-
       }
 
       if (showViewer_) {
@@ -119,32 +125,30 @@ private void createDisplay(JSONObject summaryMetadata) {
       viewer_.setReadZMetadataFunction((JSONObject tags) -> AcqEngMetadata.getStageZIntended(tags));
    }
 
-   public void putImage(final TaggedImage taggedImg) {
+   public Object putImage(final TaggedImage taggedImg) {
       HashMap<String, Object> axes = AcqEngMetadata.getAxes(taggedImg.tags);
-      final Future added;
+      final Future<IndexEntryData> added;
       if (xyTiled_) {
-         added = storage_.putImageMultiRes(taggedImg.pix, taggedImg.tags, axes,
+         added = ((MultiresNDTiffAPI)storage_).putImageMultiRes(taggedImg.pix, taggedImg.tags, axes,
                  AcqEngMetadata.isRGB(taggedImg.tags),
                  AcqEngMetadata.getBitDepth(taggedImg.tags),
                  AcqEngMetadata.getHeight(taggedImg.tags),
                  AcqEngMetadata.getWidth(taggedImg.tags));
       } else {
-         added = null;
-         storage_.putImage(taggedImg.pix, taggedImg.tags, axes,
+         added = storage_.putImage(taggedImg.pix, taggedImg.tags, axes,
                  AcqEngMetadata.isRGB(taggedImg.tags),
                  AcqEngMetadata.getBitDepth(taggedImg.tags),
                  AcqEngMetadata.getHeight(taggedImg.tags),
                  AcqEngMetadata.getWidth(taggedImg.tags));
       }
 
-
       if (showViewer_) {
          //put on different thread to not slow down acquisition
          displayCommunicationExecutor_.submit(new Runnable() {
             @Override
             public void run() {
                try {
-                  if (added != null) {
+                  if (xyTiled_) {
                      // This is needed to make sure multi res data at higher
                      // resolutions kept up to date I think because lower resolutions
                      // aren't stored temporarily. This could potentially be
@@ -165,6 +169,11 @@ public void run() {
             }
          });
       }
+      try {
+         return added.get();
+      } catch (Exception e) {
+         throw new RuntimeException(e);
+      }
    }
 
    ///////// Data source interface for Viewer //////////
@@ -177,9 +186,13 @@ public int[] getBounds() {
    public TaggedImage getImageForDisplay(HashMap<String, Object> axes, int resolutionindex,
            double xOffset, double yOffset, int imageWidth, int imageHeight) {
 
-      return storage_.getDisplayImage(
-              axes, resolutionindex, (int) xOffset, (int) yOffset,
-              imageWidth, imageHeight);
+      if (storage_ instanceof MultiresNDTiffAPI) {
+         return ((MultiresNDTiffAPI) storage_).getDisplayImage(
+                 axes, resolutionindex, (int) xOffset, (int) yOffset,
+                 imageWidth, imageHeight);
+      } else {
+         return storage_.getSubImage(axes, (int) xOffset, (int) yOffset, imageWidth, imageHeight);
+      }
    }
 
    @Override
@@ -189,12 +202,17 @@ public Set<HashMap<String, Object>> getImageKeys() {
 
    @Override
    public int getMaxResolutionIndex() {
-      return storage_.getNumResLevels() - 1;
+      if (storage_ instanceof MultiresNDTiffAPI) {
+         return ((MultiresNDTiffAPI) storage_).getNumResLevels() - 1;
+      }
+      return 0;
    }
 
    @Override
    public void increaseMaxResolutionLevel(int newMaxResolutionLevel) {
-      storage_.increaseMaxResolutionLevel(newMaxResolutionLevel);
+      if (storage_ instanceof MultiresNDTiffAPI) {
+         ((MultiresNDTiffAPI) storage_).increaseMaxResolutionLevel(newMaxResolutionLevel);
+      }
    }
 
    @Override